tools

Molecular Maya
(mMaya) is a free plugin for Autodesk Maya that lets users import, model and animate molecular structures. We leverage the power and flexibility of Maya while offering innovative, intuitive tools specialized for the challenges of molecular modeling and animation. mMaya is further enhanced by a series of 'kits' that expand its functionality and greatly streamline molecular modeling, animation, and simulation (see below).

Molecular Maya's Modeling kit enables the rapid and intuitive creation of structurally accurate and simulation-ready macromolecular models. Many if not most 3D structures in databases such as the PDB are incomplete and, although primary structure is often known, truncations and gaps are common occurrences. The mMaya Modeling kit facilitates the creation of full-length molecular models by automating the process of finding and filling such gaps, giving the user control over secondary structure and dynamic control over posing newly synthesized polypeptide chains. The kit also provides easy chain alignment, splitting and PDB export tools, as well as a library of common protein domains to streamline the molecular modeling process.

Molecular Maya's Cytoskeleton kit enables intuitive and rapid modeling of structurally-accurate actin or microtubule fibers (an intermediate filament model is also included). Deformable models are created either from user-generated curves or using a procedural modeling 'volume populator' approach. Users can customize 'level of detail' (LOD) controls for fiber geometry and curve fitting , which leads to efficient viewport handling, 'a must' for the manipulation of large fiber arrays. Strand mounts allow users to bind and move elements along individual fibers to facilitate animation of cytoskeleton-interacting proteins.

Similarly, Colonia Periférico is judged perversely impermeable to the ministrations of state management and as entangled in substances that are designated as harmful—drugs, bacteria, soda—but that provide persistence through social stability. In the American South, toxicity both protected and poisoned enslaved workers on indigo plantations; in Mexico City, toxicity prevents surveillance and violence for Colonia Periférico and its residents, even as it may make people sick. Within the standard public health and social work frames of resilience, it is difficult for state actors to imagine these toxic entanglements as protective. The problem with resilience is that it partakes in individualizing logics by leaving larger structures unaddressed. I worry, though, about entanglement as an alternative, because it may not provide much more solace than resilience to those who live amid the toxins.

By August 2016 Alma was trying to drink less soda. This might seem like a public health victory, but the lesson is not so clear. At a routine clinic visit in July, Alma and her husband Juan had both been diagnosed as prediabetic. Laughing, Alma and Juan narrated the inexplicability of this diagnosis. Juan is heavy, but has rarely drunk soda or eaten sweets. Unlike Alma, he does not spend his life inside Colonia Periférico. He works six days a week outside the
colonia
installing commercial security systems, a salaried, fairly stable job. And yet Juan is just as prediabetic as Alma, who has a sweet tooth with a vengeance. “You know me,” she says, “always with my candy”; she mimes dipping into a bag of sweets. The lack of sense in Juan’s diagnosis prompts questions. Why quit soda when prediabetes can arrive without it? How do you change your diet to prevent diabetes if you do not eat sweets? These uncertainties underscore something increasingly clear in nutrition, exposure science, and toxicology: substances do not have reliable, explicable, or linear effects.

To isolate variables that document linear effects, knowledge claims, and public policy recommendations about chemicals and nutrition in the life sciences and in public health are based on large samples that become numbers. As anthropologists and STS scholars committed to entanglement and uncertainty, we know linear thinking constitutes a problem. Linear thinking shuts down the possibility of tracing how chemicals might be engaged in looping relations with bodies situated in their specific worlds (
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). As
Michelle Murphy (2004
, 267) argues, focusing on a single signal, a single variable, a single chemical entails a “learned inattention to other noise.” Linearity is modernity itself, delinking the chains that bind to make new autonomous objects. It is important, then, to foreground a critique of the isolationist, linear tendencies baked into environmental and public health. These tendencies tend to universalize bodies while individualizing behavior—for instance, in anti-obesity campaigns that fail to account for a radically transformed food landscape and the multiple destabilizations of NAFTA and the War on Drugs, and in chemical-exposure studies that decontextualize lead from poverty (
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).